Parallel & Distributed Computing

HPC Cluster Configuration

This documentation will help you create a hpcc system on vmware.
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Tutorial · Softwares · Issues

Project Report

Section: BSCS 7A

Syed Mustafa Imam

Syed Hurrar Hassan Rizvi

Elliott Franscis Joseph

Hirdesh Kumar

Table of contents

1.Introduction to HPC Cluster
2.Use Cases
3.Steps

1.Introduction to HPC Cluster

HPC Cluster is a collection of hundreds or thousands of servers that are networked together, each server is known as a node. Each node in a cluster works in parallel with each other, boosting processing speed to deliver high-performance computing. HPC is appropriate for most small and medium-sized businesses since these nodes are tightly, this is the reason why it is called a cluster. All cluster nodes have the same components as a laptop or desktop such as the CPU, cores, memory, and storage space. The difference between a personal computers and a cluster node is in quantity, quality, and power of the components. User login to the cluster head node is done by using the ssh program.

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2.Use Cases

HPC is deployed on-premises, at the edge, or in the cloud. HPC solutions are used for a variety of purposes across multiple industries. HPC is used to help scientists find sources of renewable energy, understand the evolution of our universe. Predict and track the storms, and create new materials.

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Research Labs

HPC is used to help scientists find sources of renewable energy, understand the evolution of our universe, predict and track storms and create new materials.

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Media And Entertainment

HPC is used to edit feature films, render mind-blowing visual effects, and stream live events around the world.

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Oil and gas

HPC is used to more accurately identify where to drill for new oil wells and to help boost production from existing oil wells.

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Artificial Intelligence

HPC is used to detect credit card fraud, provide self-guided technical support, self-driving vehicles, and improve cancer screening techniques.

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Financial Services

HPC is used to track real-time stock trends and automate trading.

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3.Steps

Creation Of Virtual Machines

The master node is set up by the name 'HPC Master' with CentOS-5 32 bit as the main OS of the Virtual Machine and the network working on a NAT. The system configuration of our HPC masternode is presented below:

The compute node is also created by the name 'node1' with CentOS-5 32 bit as the main OS of the Virtual Machine with a standard data store and a NAT. The system configuration of the node1 are presented below:

Another compute node is also created by the name 'node2' with Centos-5 32 bit as the main OS of the Virtual Machine with a standard data store and a NAT. The system configuration of the node2 are presented below:

An NTP server was also created by using a node that is not part computation performed by a cluster. It was done by using Ubuntu OS 64 bit as the main OS of the Virtual Machine with a standard data store and a NAT network. System configurations are presented below:

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Linux Installation on nodes

You can download the iso image of CentOS 5.2 here:https://archive.org/details/cent-os-5.2-i-386-bin-dvd

After booting up from the image it will automatically go into the install node.

Once it asks for input, press skip for skipping the media check.

Create a custom layout then add a partition with file type swap and size of 128MB and additional size options as fixed size , then press ok.

Repeat the process one more time to create another partition with ext3 file type and size of 128MB and additional size options as fixed to maximum allowable size , then press ok.

Once we have a disk that is all you need. It's going to have the hostname manually entered as the master node, then press edit above and uncheck Enable IPv6 support. Change dynamic IP to manual IP as 192.168.174.142 and prefix/netmask as 255.255.255.0 then press okay then press next then again next then continue as We don't want any gateway no DNS and let's specify our timezone, so press next.

Specify the password as abc.123 then press next.

Uncheck desktop and just click customize now by select packages from the options. We don't requir a desktop. We want editors , development libraries, and development tools. Go to the base system, uncheck dial network support.

So that is all you will need right now. so just go to next. Press Next to start the installation and so on, we will be done.

Once the system is completely installed, select reboot.

Remember that your nodes in your HPC cluster should be of the same hardware, same processor architecture, and the same version of the operating system you're using.

Let your system boot up. So this is how you would install CentOS 5.

On a virtual machine now we've two more nodes to go on which we need to install the Linux operating system. Once we' have our desired configurations of the system, we will copy the files from the backend. This is because we have VMware Workstaion Pro 16 that does not support cloning. So what we will be doing is shutting down this server/system/VM, and now copying its file disk file. As your server is turned off, let's go to the backend.

We have used Ubuntu as for our NTP server. You can use any distribution of Linux or Windows version for this task. After powering the Ubuntu virtual machine, select an language of your understand and press Install Ubuntu Button. Select an keyboard layout, after this choose normal installation then select earse disk and install Ubuntu option. Select an timezone and setup login credentials. Press continue and wait for the installation to complete.

From our hostmachine console we modify the folders of Virtual Machines files.

You can download the nodes here:https://drive.google.com/drive/folders/1P3KzqFtmWejV8prhWgSvIFon_LInhR_g?usp=sharing

Command:

[root@hostmachine ~]# cd machines

Command:

[root@hostmachine machines]# ls

And we have this HPC masternode directory, which we have these files.

Let's enter into this directory by,

Command:

[root@hostmachine machines]# cd masternode

Command:

[root@hostmachine masternode]# ls

Command:

[root@hostmachine masternode]# ls -lh

As you can see, this is your virtual machine disk file named masternode.vmdk .

So now we'll copying this file.

Command:

[root@hostmachine masternode]# ls -lh ../node1/

As you can see you have four files there. Now we will copy this VMDK file from here and overwrite this VMDK file here.

Command:

[root@hostmachine masternode]# cp masternode.vmdk ../node1/node1.vmdk

Press y for yes overwriting.

As you can see the file is copied so let's check the list.

Command:

[root@hostmachine masternode]# ls ../node1/ -lh

Let's try starting node1 and see what happens. Click power on and go to the console window and let it boot up. It will have all settings from your masternode. That means it will also have the same hostname, same IP everything.

Once this is booted up. So let's go to the console, it will seem like a master node, but it is not it is, as you can see here, this is node1 and in the same way, we'll do the node2 as well. But first, adjust the hostnames.

Command:

[root@masternode ~]# vi /etc/sysconfig/network

Then edit hostname as node1 and the IP is going to be.

Command:

[root@masternode ~]# vi /etc/sysconfig/network-scripts/ifcfg-eth0

First Ethernet network interface card or NIC in the system should not get its IP from DHCP. It's going to be a static IP address equal to 192.168.174.143 and netmask is equal to 255.255.255.0

One more thing to see hosts.

Command:

[root@masternode ~]# vi /etc/hosts

Remove this master node at all from the script.

Now let's change the hostname manually.

Command:

[root@masternode ~]# hostname node1

Command:

[root@masternode ~]# service syslog restart

Command:

[root@masternode ~]# less /var/log/messages

It will make sure that the logs in the various log messages are written correctly.

Press shift G you can see as soon as you've restarted syslog the logs here it says node1 now before it was masternode.

Then reboot this system.

Command:

[root@masternode ~]# reboot

Now repeat the same process for node2 as you have done for the node1.

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Configuring etc host file

Command:

[root@masternode ~]# vi /etc/hosts

Now delete IP version 6 naming file.

Then remove a masternode from this localhost line.

Add three lines here

192.168.174.142 masternode

192.168.174.143 node1

192.168.174.145 node2

Then save the these changes and return to the console.

Command:

[root@masternode ~]# scp /etc/hosts node1:/etc/

Except for the fingerprint of node1, node1's password is abc.123.

Do the same thing for node2.

Command:

[root@masternode ~]# scp /etc/hosts node2:/etc/

Except for the fingerprint of node2, node2's password is abc.123.

Now, the, etc hosts file is configured.

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SSH equivalence establishment for user root

Now we will generate public and private keys (DSA and RSA) of all nodes.

Generate DSA keys.

Command:

[root@masternode ~]# ssh-keygen -t dsa

Just press enter, no need to enter a passphrase.

Now generate the RSA keys.

Command:

[root@masternode ~]# ssh-keygen -t rsa

Just press enter, no need to enter a passphrase.

Now if you want you can check these keys.

Command:

[root@masternode ~]# cd .ssh/

Command:

[root@masternode .ssh]# ls -l

As you can see both DSA and RSA are visible along with the public and private keys.

Now copy all four key files for this directory

Command:

[root@masternode .ssh]# cd ..

Command:

[root@masternode ~]# scp -r .ssh node1:/root/

Enter the password which is redhat

As files are copied in node 1 now do the same process for node 2.

Command:

[root@masternode ~]# scp -r .ssh node2:/root/

Now do one more step

Command:

[root@masternode ~]# cd .ssh/

Command:

[root@masternode .ssh]# cat *.pub >> authorized\_keys

Command:

[root@masternode .ssh]# cd ..

Now copy these files on both nodes again

Command:

[root@masternode ~]# scp -r .ssh node1:/root/

Enter the password which is redhat

As files are copied in node 1 now do the same process for node 2.

Command:

[root@masternode ~]# scp -r .ssh node2:/root/

Now We will generate RSA fingerprints,

Command:

[root@masternode ~]# ssh-keyscan -t dsa masternode node1 node2

Now I'm going to put it in a special file on this log

Command:

[root@masternode ~]# ssh-keyscan -t dsa masternode node1 node2 > /etc/ssh/ssh_known_hosts

You see this file. This file is a valid one, but it does not exist by default. Now what I'm going to do is I'm going to scan the RSA keys of the same nodes and I'm going to append that to this file.

Command:

[root@masternode ~]# ssh-keyscan -t rsa masternode node1 node2 >> /etc/ssh/ssh_known_hosts

Now see how the file looks like,

Command:

[root@masternode ~]# less /etc/ssh/ssh_known_hosts

Now replicate this file to all nodes.

Command:

[root@masternode ~]# scp /etc/ssh/ssh_known_hosts node1:/etc/ssh

Command:

[root@masternode ~]# scp /etc/ssh/ssh_known_hosts node2:/etc/ssh

Testing by logging it into each node

Command:

[root@masternode ~]# ssh masternode

Command:

[root@masternode ~]# exit

Command:

[root@node1 ~]# ssh node1

Command:

[root@node1 ~]# exit

Command:

[root@masternode ~]# ssh node2

Command:

[root@node2 ~]# exit

Testing by logging all nodes into each other node

Command:

[root@node1 ~]# ssh masternode uptime

Command:

[root@node1 ~]# ssh node1 uptime

Command:

[root@node1 ~]# ssh node2 uptime

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Setup NTP Service

Setup NTP in Ubuntu

Update our local repository

Command:

[root@linux ~]# apt-get update

Install NTP server daemon.

Command:

[root@linux ~]# apt-get install ntp

Switch to an NTP server pool closest to your location

Command:

[root@linux ~]# vi /etc/ntp.conf

In this file, you will be able to see a pool list.

Use servers from the NTP Pool Project. Approved by Ubuntu Technical Board on 2011-02-08 (LP: #104525). See http://www.pool.ntp.org/join.html for more information.

Add the following lines if not added automatically.

pool 0.ubuntu.pool.ntp.org iburst pool 1.ubuntu.pool.ntp.org iburst pool 2.ubuntu.pool.ntp.org iburst pool 3.ubuntu.pool.ntp.org iburst

Exit the file.

Restart the NTP server.

Command:

[root@linux ~]# service ntp restart

Check NTP server status.

Command:

[root@linux ~]# service ntp status

Configure Firewall to allow nodes access to NTP server

Command:

[root@linux ~]# ufw allow from any to any port 123 proto udp

Command:

[root@linux ~]# ip a

The IP address of Ubuntu is 192.168.174.131, so NTP server IP would be same.

Install NTP service on masternode.

Command:

[root@masternode ~]# rpm –-import /etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5

Command:

[root@masternode ~]# yum -y install ntp

Command:

[root@masternode ~]# scp node1:/etc/yum.repos.d/CentOS-Base.repo .

Command:

[root@masternode ~]# scp node1:/etc/yum.repos.d/CentOS-Base.repo /etc/yum.repos.d/

Install NTP service on node2.

Command:

[root@node2 ~]# rpm –-import /etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5

Command:

[root@node2 ~]# scp node1:/etc/yum.repos.d/CentOS-Base.repo /etc/yum.repos.d/

Command:

[root@node2 ~]# yum -y install ntp

Install NTP service on node1.

Command:

[root@nodeq ~]# rpm –-import /etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5

Command:

[root@node1 ~]# yum -y install ntp

Configuration

NTP configuration masternode,node1,node2.

Command:

[root@masternode ~]# vi /etc/ntp.conf

Add server 192.168.174.131 which is our host machine.

Comment server 0, server 1, server 2

Comment server local-clock and fudge

Exit the file

Command:

[root@masternode ~]# chkconfig --level 35 ntpd on

Restart service

Command:

[root@masternode ~]# service ntpd restart

Command:

[root@masternode ~]# ntpq -p -n

Command:

[root@masternode ~]# watch "ntpq -p -n"

Command:

[root@masternode ~]# scp /etc/ntp.conf node1:/etc/ntp.conf

Command:

[root@node1 ~]# chkconfig --level 35 ntpd on

Restart service

Command:

[root@node1 ~]# service ntpd restart

Command:

[root@node1 ~]# ntpq -p -n

Command:

[root@node1 ~]# watch "ntpq -p -n"

Command:

[root@node1 ~]# scp /etc/ntp.conf node2:/etc/ntp.conf

Command:

[root@node2 ~]# chkconfig --level 35 ntpd on

Restart service

Command:

[root@node2 ~]# service ntpd restart

Command:

[root@node2 ~]# ntpq -p -n

Command:

[root@node2 ~]# watch "ntpq -p -n"

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Installation of PDSH

Check if pdsh is downloaded on the host machine or not.

Command:

[root@linux linux]# cd

Command:

[root@linux ~]# ls

If it is not downloaded you can download it from the SourceForge website by typing pdsh on google search.

Now copy pdsh from masternode

Command:

[root@masternode ~]# scp 192.168.174.131:/root/pdsh* .

Type yes

Enter the password which is abc.123,

PDSH is now copied.

Rebuild rpm

Command:

[root@masternode ~]# rpmbuild –rebuild pdsh-2.18-1.src.rpm

This is not mandatory for all nodes other than masternode

Changing directory

Command:

[root@masternode ~]# cd /usr/src/redhat/RPMS/i386/

Command:

[root@masternode i386]# rpm -ivh pdsh-*

Now wait until it is debugging and installing

Now everything is installed and pdsh works.

What does pdsh do? If you want to perform a certain operation on all the nodes, or any specific nodes, one way is to manually log in through SSH to each node and perform the task and the second is you can just tell PD shell to do it at will go out and perform that task on all the nodes. It's very simple. So suppose you want to execute the date command on all the nodes or uptime command on all the nodes or whatever. So you would just tell PD shell to do it but in order for PD shell to work, it needs a machine file.

Command:

[root@masternode i386]# vi /etc/machines

Add these three lines

masternode

node1

node2

These are the three nodes that I'm going to use or which will be used for PD shall.

Now execute the pdsh on all nodes.

What executes what let's say date, is simple.

Command:

[root@masternode i386]# pdsh -a date

It went out on all the nodes and it brought the output back from all the notes you see it they're all 100% At the same time that's not the because of PDSH because of NTP which we just set up you Just go to masternode and enter.

Command:

[root@masternode i386]# pdsh -a ntpq -p -n

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Setup NFS

Now setup nfs on masternode

Coming back to home directory

Command:

[root@masternode i386]# cd

Command:

[root@masternode ~]# vi /etc/exports/

Add

/cluster       *(rw,no_root_squash,sync)

Save and exit

Restart NFS service

Command:

[root@masternode ~]# service nfs restart

Check Configuration

Command:

[root@masternode ~]# chkconfig -–level 35 nfs on

Make a directory

Command:

[root@masternode ~]# mkdir /cluster

Again restart service

Command:

[root@masternode ~]# service nfs restart

Now we have to create this directory on all nodes so we will just use pdsh to create on all nodes at once

Command:

[root@masternode ~]# pdsh -w node1,node2 mkdir /cluster

Now mounting

Command:

[root@node1 yum.repos.d]# df -hT

Execute this command on node1

Command:

[root@node1 yum.repos.d]# mount -t nfs masternode:/cluster /cluster/

Execute this command on node2

Command:

[root@node2 ~]# mount -t nfs masternode:/cluster /cluster/

Now you can see that it is written that you have mounted it from the masternode.

Now specify etc/fstab on node1

Command:

[root@node1 ~]# vi /etc/fstab

Add this line

masternode:/cluster /cluster  nfs defaults  0 0

Kindly disable firewall in masternode,node1 and node2.

Now specify etc/fstab on node2

Command:

[root@node2 ]# vi /etc/fstab

Add this line

masternode:/cluster /cluster nfs defaults 0 0

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Creation of ordinary user and also setup SSH equivalence

Group: mpigroup-600

User: mpiuser-600

Member of mpigroup

The home directory will be /cluster/mpiuser

Now coming back to the masternode.

Command:

[root@masternode ~]# groupadd -g 600 mpigroup

Command:

[root@masternode ~]# useradd -u 600 -g 600 -d /cluster/mpiuser mpiuser

This directory is now created.

Now add group and users on node1 and node2

Run these commands on each node separately

Command:

[root@node1 ~]# groupadd -g 600 mpigroup

[root@node1 ~]# useradd -u 600 -g 600 -d /cluster/mpiuser mpiuser

Command:

[root@node2 ~]# groupadd -g 600 mpigroup

[root@node2 ~]# useradd -u 600 -g 600 -d /cluster/mpiuser mpiuser

Our users and groups are now created on all nodes.

Now we are setting up SSH user equivalence for MPI to funciton properly.

Command:

[root@masternode ~]# su - mpiuser

Generate its sshkeys as well

Command:

[mpiuser@masternode ~]$ ssh-keygen -t dsa

Press enter no need to enter paraphrase

Command:

[mpiuser@masternode ~]$ ssh-keygen -t rsa

Press enter no need to enter paraphrase

As two key pairs are generated

Now,

Command:

[mpiuser@masternode ~]$ ls /cluster/

Switch to mpiuser from node1

Command:

[root@node1 ~]# su - mpiuser

Command:

[mpiuser@node1 ~]$ ls -l

Check all the files here

Command:

[mpiuser@node1 ~]$ ls -la

Now changing directory

Command:

[mpiuser@node1 ~]$ cd .ssh/

Command:

[mpiuser@node1 .ssh]$ ls -la

Remember /cluster directory is shared across all nodes.

Append the public keys into the authorized keys file

Command:

[mpiuser@masternode .ssh]$ cat *.pub >> authorized_keys

Command:

[mpiuser@masternode .ssh]$ cd ..

Now try to command as a mpiuser on all nodes

Command:

[mpiuser@masternode ~]$ ssh masternode uptime

Command:

[mpiuser@masternode ~]$ ssh node1 uptime

Command:

[mpiuser@masternode ~]$ ssh node2 uptime

Check hostname by ssh command

Command:

[mpiuser@masternode ~]$ ssh masternode hostname

Command:

[mpiuser@masternode ~]$ ssh node1 hostname

Command:

[mpiuser@masternode ~]$ ssh node2 hostname

Hostnames of each node must be visible by these commands.

Now check hostnames by PDSH

Command:

[mpiuser@masternode ~]$ pdsh -a hostname

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Installation of prerequisites packages (GCC, G77, etc)

Check if all nodes have GCC or not

Command:

[root@masternode ~]# rpm -q GCC

The version of GCC will be visible

Command:

[root@masternode ~]# rpm -qa | grep g77

If not shown by this command you can run

Command:

[root@masternode ~]# yum list | grep g77

If g77 exists this will be visible there.

Install g77 on masternode

Command:

[root@masternode ~]# yum -y install compat-gcc-34-g77

Installing g77 on node1 and node2 from masternode

Command:

[root@masternode ~]# pdsh -w node1,node2 yum -y install compat-gcc-34-g77

All prerequisites are now installed.

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Installation of MPI

Now, we go for MPI installation.

So, MPI is basically Message Passing Interface is the language that is used to run a program specially designed program on multiple compute nodes on multiple nodes. MPI can be downloaded from various places there is open MPI this there are other MPI as well. I'm going to download it from the web.

Command:

[mpiuser@masternode ~]$ scp root@10.0.0.2:/root/mpi* .

Press yes

Enter password redhat

Mpi is downloaded in the home directory

Command:

[mpiuser@masternode ~]$ ls -lh

The file is not owned by mpiuser

Command:

[root@masternode /]# chown mpiuser:mpigroup /cluster -R

Access is now given to mpiuser

Switch user to mpiuser

Command:

[root@masternode /]# su - mpiuser

Moving mpi

Command:

[mpiuser@masternode ~]$ mv mpich2-1.0.8.tar.gz ..

Command:

[mpiuser@masternode ~]$ ls

Command:

[mpiuser@masternode ~]$ cd ..

Command:

[mpiuser@masternode cluster]$ ls -lh

As you can see it is nowhere.

Now uncompressing

Command:

[mpiuser@masternode cluster]$ tar xzf mpich2-1.0.8.tar.gz

Command:

[mpiuser@masternode cluster]$ ls

Command:

[mpiuser@masternode cluster]$ cd mpich2-1.0.8

Command:

[mpiuser@masternode mpich2-1.0.8]$ ls

There are so many files we are now configuring.

This will be a new directory.

Command:

[mpiuser@masternode mpich2-1.0.8]$ ./configure –-prefix=/cluster/mpich2

All the parts which were left during the installation will be installed by this command.

Command:

[mpiuser@masternode mpich2-1.0.8]$ make

Now the files will move to /cluster directory

Command:

[mpiuser@masternode mpich2-1.0.8]$ make install

next, I'm going to set up some environment variables in the MPI user's bash_profile.

First goto home directory

Command:

[mpiuser@masternode mpich2-1.0.8]$ cd

Command:

[mpiuser@masternode ~]$ vi .bash_profile

Add these lines there

PATH=$PATH:$HOME/bin:/cluster/mpich2/bin

LD\_LIBRARY\_PATH=$LD\_LIBRARY\_PATH:/cluster/mpich2/lib

export PATH

export LD\_LIBRARY\_PATH

If you don't want to logout

Command:

[mpiuser@masternode ~]$ source .bash_profile

This will load the new values

You can also verify by the echo command

Command:

[mpiuser@masternode ~]$ echo $PATH

Check if it is able to find MPD

Command:

[mpiuser@masternode ~]$ which mpd

Check if it is able to find mpiexec

Command:

[mpiuser@masternode ~]$ which mpiexec

Check if it is able to find mpirun

Command:

[mpiuser@masternode ~]$ which mpirun

Create an mpd.host file

Command:

[mpiuser@masternode ~]$ cat >> /cluster/mpiuser/mpd.hosts << EOF

> masternode

> node1

> node2

> EOF

Check the names here of all nodes

Command:

[mpiuser@masternode ~]$ cat /cluster/mpiuser/mpd.hosts

masternode

node1

node2

If you don't want your masternode to take part in any kind of computation follow the command below.

Command:

[mpiuser@masternode ~]$ vi /cluster/mpiuser/mpd.hosts

Remove masternode from here and exit

Now creating a secret file

Command:

[mpiuser@masternode ~]$ vi /cluster/mpiuser/.mpd.conf

Add this line

secretword=redhat

Save and exit

Boot mpt on compute nodes

Command:

[mpiuser@masternode ~]$ mpd &

If it has permission issue follow below command

Command:

[mpiuser@masternode ~]$ chmod 0600 /cluster/mpiuser/.mpd.conf

Command:

[mpiuser@masternode ~]$ ps aux | grep mpd

Now again Booting mpt on compute nodes

Command:

[mpiuser@masternode ~]$ mpd &

Checking if it's running

Command:

[mpiuser@masternode ~]$ mpdtrace -l

Exit all

Command:

[mpiuser@masternode ~]$ mpdallexit

Command:

[mpiuser@masternode ~]$ mpdboot -n 2 --chkuponly

Now you can see 2 hosts are up

Command:

[mpiuser@masternode ~]$ ps aux | grep mpd

Now edit this file

Command:

[mpiuser@masternode ~]$ vi /cluster/mpiuser/mpd.hosts

Add this line

Masternode

Save and exit

Checking how many servers are up

Command:

[mpiuser@masternode ~]$ mpdboot -n 3 --chkuponly

Now you can see 3 hosts are up

Command:

[mpiuser@masternode ~]$ mpdboot -n 3

Command:

[mpiuser@masternode ~]$ mpdtrace

Now exit from all

Command:

[mpiuser@masternode ~]$ mpdexitall

Now check if I am traced or not

Command:

[mpiuser@masternode ~]$ mpdtrace

Run each command separately and see the time difference

Command:

[mpiuser@masternode ~]$ cd ..

[mpiuser@masternode cluster]$ cd mpich2-1.0.8/examples

[mpiuser@masternode examples]$ mpiexec -n 1 ./cpi

As you can see execution time

Command:

[mpiuser@masternode examples]$ mpiexec -n 2 ./cpi

Command:

[mpiuser@masternode examples]$ mpiexec -n 3 ./cpi

Compiling a program

Command:

[mpiuser@masternode examples]$ mpicc -o icpi icpic.c

Command:

[mpiuser@masternode examples]$ ls

It's compiled.

Command:

[mpiuser@masternode examples]$ mpiexec -n 1 ./icpi

Enter any large random number and see the execution time.

Now run this using 2 nodes

Command:

[mpiuser@masternode examples]$ mpiexec -n 1 ./icpi

Enter the same number and see the execution time difference.

On virtual machines, it might give higher time but in physical servers, it will be okay sometimes it gets problematic in VM's.

Remember real hardware clusters will give much accuracy and proficiency.

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Compiling Linpack

For linpack, you would need a BLAS library.

Downlad the gotoblas library from here: https://www.tacc.utexas.edu/documents/1084364/1087496/GotoBLAS2-1.13.tar.gz/b58aeb8c-9d8d-4ec2-b5f1-5a5843b4d47b

You can download in the host machine and then copy it to master node.

Command:

[root@hostmachine ~]# scp  -r GotoBLAS2-1.13.tar.gz root@10.0.0.20:/masternode/

Enter root's password

Now go to the master node and check it.

Command:

[root@masternode ~]# ls

Copy file

Command:

[root@masternode ~]# cp GotoBLAS2-1.13.tar.gz /cluster/mpiuser/

Switching user

Command:

[root@masternode ~]#  su - mpiuser

Command:

[mpiuser@masternode ~]# ls -al

Uncompressing

Command:

[mpiuser@masternode ~]# tar xzf GotoBLAS2-1.13.tar.gz

It will create a directory here

Command:

[mpiuser@masternode ~]# cd GotoBLAS3-1.13

As it is seen, a directory is created.

BLAS is a linear algebra library

Command:

[mpiuser@masternode GotoBLAS3-1.13]# ls

Command:

[mpiuser@masternode GotoBLAS3-1.13]# make BIN=32

Command:

[mpiuser@masternode GotoBLAS3-1.13]#  gmake TARGET=NEHALEM

It is compiled now.

Now you would need to download a high-performance linpack.

You can download it from www.netlib.org/benchmark/hpl

Now copy it from the host machine

Command:

[root@hostmachine ~]# scp -r hpl-2.3.tar.gz mpiuser@10.0.0.20:/cluster/mpiuser/

Enter password:

Check now if the file is here

Command:

[mpiuser@masternode ~]# ls

The file is in the home directory of this mpiuser.

Extract or uncompress

Command:

[mpiuser@masternode ~]# tar xzf hpl.tgz

Command:

[mpiuser@masternode ~]# ls

Command:

[mpiuser@masternode ~]# cd hpl

Command:

[mpiuser@masternode ~]# ls

Copying setup

Command:

[mpiuser@masternode hpl]# cp setup/Make.Linux_pII_FBLAS_gm .

Copying to the current location

Check your GCC version

Command:

[mpiuser@masternode hpl]#  gcc -v

Select version

Command:

[mpiuser@masternode hpl]# cd /usr/lib/gcc/i386-redhat-linux/4.1.2/

Check current location

Command:

[mpiuser@masternode 4.1.2]#  pwd

Command:

[mpiuser@masternode hpl]# vi Make.Linux_PII_FBLAS_gm

Change LA Directory in this file to

$ (HOME) / GotoBLAS

Change LA Library

$ (LAdir)/libgoto.a -lm -L/usr/lib/gcc/i386-redhad-linux/4.1.2

Change CC Flags

$ (HPL_DEFS) -03

Change Linker

$ mpicc

Save and exit

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Benchmarking

Now build this

Command:

[mpiuser@masternode hpl]#  make arch=Linux_PII_FBLAS_gm

Moving to this directory

Command:

[mpiuser@masternode hpl]# cd /cluster/mpiuser/hpl/bin/Linux_PII_FBLAS_gm/

List here

Command:

[mpiuser@masternode Linux_PII_FBLAS_gm]# ls

Copy HPL.dat

Command:

[mpiuser@masternode Linux_PII_FBLAS_gm]# cp HPL.dat HPL.dat.orig

Command:

[mpiuser@masternode Linux_PII_FBLAS_gm]# vi HPL.dat

Now the linpack configuration file has appeared.

value from size can be found first, nothing to change.

Command:

[mpiuser@masternode Linux_PII_FBLAS_gm]# free -b

Go to calculator on node2

Command:

[root@node2 ~]# bc

< Sqrt (.1\*(value of the output of your free b) \* 2)

> 5997.8 approx 6000

Now edit this file on master node

Command:

[mpiuser@masternode Linux_PII_FBLAS_gm]# vi HPL.dat

Edit No of problem to 1

Size 6000

No of block 1

Size of block 100

Process grid 1

The processor on each node 1

Processor quantity 2

Save and exit

First exit

Command:

[mpiuser@masternode Linux_PII_FBLAS_gm]# mpdallexit

Boot again:

Command:

[mpiuser@masternode Linux_PII_FBLAS_gm]# mpdboot -n 2

Now execute hpl program

Command:

[mpiuser@masternode Linux_PII_FBLAS_gm]# mpiexec -n 2 ./xhpl

This is our benchmarking being started. This might take some time.

You can see complete passing and failing reports at the end of the benchmarking process.

Now execute hpl programe and send output to textfile

Command:

[mpiuser@masternode Linux_PII_FBLAS_gm]# mpiexec -n 2 ./xhpl > performance.txt

hirdeshkumar2407/HPCC-On-VMware-

HPC Cluster Configuration

1.Introduction to HPC Cluster

2.Use Cases

Research Labs

Media And Entertainment

Oil and gas

Artificial Intelligence

Financial Services

3.Steps

Creation Of Virtual Machines

Linux Installation on nodes

Configuring etc host file

SSH equivalence establishment for user root

Setup NTP Service

Installation of PDSH

Setup NFS

Creation of ordinary user and also setup SSH equivalence

Installation of prerequisites packages (GCC, G77, etc)

Installation of MPI

Compiling Linpack

Benchmarking